The story of Marvel Super Heroes: War of the Gems takes place in a fantasy world where magical gems have been stolen by an evil force. The player must control one of eight heroes, each with their own unique abilities, to retrieve the gems and defeat the villainous forces.
The gameplay involves action-packed battles against hordes of enemies, as well as exploration and puzzle-solving. Players can switch between their heroes on the fly using a special button, allowing for creative combinations of attacks and strategies.